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Fix duplicate metabolites identified by MetaNetX IDs #653

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Fix duplicate metabolites identified by MetaNetX IDs #653

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543c1ba
fix-remove mets and rxns
JHL-452b Jun 19, 2023
5fbc4d4
fix-change MetaNetX ID annotations
JHL-452b Jun 19, 2023
0c28ca2
fix-replace mets
JHL-452b Jun 19, 2023
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7 changes: 6 additions & 1 deletion data/deprecatedIdentifiers/deprecatedMetabolites.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -2203,4 +2203,9 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM03573m" "MAM03573" "etfox" "" "" "" "" "" "" "" "etfox" "MNXM11479" "" "etfox_m"
"MAM03574m" "MAM03574" "etfrd" "" "" "" "" "" "" "" "etfrd" "MNXM11480" "" "etfrd_m"
"MAM03494c" "MAM03494" "c3dc" "" "" "" "22833583" "" "" "" "c3dc" "" "" "c3dc_c"
"MAM03494e" "MAM03494" "c3dc" "" "" "" "22833583" "" "" "" "c3dc" "" "" "c3dc_s"
"MAM03494e" "MAM03494" "c3dc" "" "" "" "22833583" "" "" "" "c3dc" "" "" "c3dc_s"
"MAM03684e" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_s"
"MAM03684x" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_p"
"MAM03684m" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_m"
"MAM03684c" "MAM03684" "hxa" "" "" "CHEBI:17120" "" "" "" "" "hxa" "MNXM1653" "" "hxa_c"
"MAM00759c" "MAM00759" "" "C13712" "" "" "" "LMST02030130" "" "" "M00759" "MNXM3494" "m00759c" "m00759c"
3 changes: 3 additions & 0 deletions data/deprecatedIdentifiers/deprecatedReactions.tsv
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Expand Up @@ -111,3 +111,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR20015" "R02549" "ABUTD;ABUTDm;R_ABUTD;R_ABUTDm" "" "" "" "" "MNXR95191" "" "" "" 0 "RHEA:19105" "" ""
"MAR20014" "R03283" "R_TMABADH;TMABADH" "" "" "" "" "MNXR104876" "" "" "" 0 "RHEA:17985" "" ""
"MAR20052" "" "ALDD21;RE3076X;R_ALDD21;R_RE3076X" "" "" "" "" "MNXR95747" "" "" "" 0 "RHEA:44016" "" ""
"MAR09949" "" "FACOAE60" "" "" "" "HXCOAc" "MNXR99139" "" "" "" 0 "" "" "HXCOAc"
"MAR11292" "" "HXAt3" "" "" "" "HXAt3" "" "" "" "" 0 "" "" "HXAt3"
"MAR11293" "" "EX_hxa_e" "" "" "" "EX_hxa[e]" "MNXR98664" "" "" "" 0 "" "" "EX_hxa[e]"
132 changes: 29 additions & 103 deletions model/Human-GEM.yml
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Expand Up @@ -4,7 +4,7 @@
short_name: "Human-GEM"
full_name: "Generic genome-scale metabolic model of Homo sapiens"
version: ""
date: "2023-06-07"
date: "2023-06-19"
taxonomy: "9606"
github: "https://github.com/SysBioChalmers/Human-GEM"
description: "Genome-scale metabolic models are valuable tools to study metabolism and provide a scaffold for the integrative analysis of omics data. This is the latest version of Human-GEM, which is a genome-scale metabolic model of a generic human cell. The objective of Human-GEM is to serve as a community model for enabling integrative and mechanistic studies of human metabolism."
Expand Down Expand Up @@ -9961,14 +9961,6 @@
- charge: -1
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM00759c"
- name: "3alpha-hydroxy-5alpha-pregnan-20-one"
- compartment: "c"
- formula: "C21H34O2"
- charge: 0
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM00760c"
- name: "3-amino-propanal"
Expand Down Expand Up @@ -53553,14 +53545,6 @@
- charge: -1
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM03684c"
- name: "Hexanoate (N-C6:0)"
- compartment: "c"
- formula: "C6H11O2"
- charge: -1
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM03976c"
- name: "Cia-5,8, Tetradecadienoic Acid"
Expand Down Expand Up @@ -54705,22 +54689,6 @@
- charge: -1
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM03684m"
- name: "Hexanoate (N-C6:0)"
- compartment: "m"
- formula: "C6H11O2"
- charge: -1
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM03684x"
- name: "Hexanoate (N-C6:0)"
- compartment: "x"
- formula: "C6H11O2"
- charge: -1
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM02169e"
- name: "indoleacetate"
Expand Down Expand Up @@ -58993,14 +58961,6 @@
- charge: 0
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM03684e"
- name: "Hexanoate (N-C6:0)"
- compartment: "e"
- formula: "C6H11O2"
- charge: -1
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM01954c"
- name: "glcnac-alpha-1,4-core 1"
Expand Down Expand Up @@ -68001,6 +67961,22 @@
- charge: -1
- inchis: ""
- metFrom: ""
- !!omap
- id: "MAM02120x"
- name: "hexanoic acid"
- compartment: "x"
- formula: "C6H11O2"
- charge: -1
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM02120m"
- name: "hexanoic acid"
- compartment: "m"
- formula: "C6H11O2"
- charge: -1
- inchis: ""
- metFrom: "HMRdatabase"
- reactions:
- !!omap
- id: "MAR03905"
Expand Down Expand Up @@ -123754,8 +123730,8 @@
- id: "MAR02003"
- name: "3alpha-hydroxy-5alpha-pregnan-20-one:NADP+ 3-oxidoreductase (A-specific)"
- metabolites: !!omap
- MAM00759c: -1
- MAM01072c: 1
- MAM01314c: -1
- MAM02039c: 1
- MAM02554c: -1
- MAM02555c: 1
Expand Down Expand Up @@ -167720,7 +167696,7 @@
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000113396 or ENSG00000121769 or ENSG00000130304 or ENSG00000135218 or ENSG00000143554 or ENSG00000145384 or ENSG00000163586 or ENSG00000164434 or ENSG00000164687 or ENSG00000167114 or ENSG00000170231 or ENSG00000170323 or ENSG00000197416 or ENSG00000205186"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- rxnFrom: "HMRdatabase;Recon3D"
- eccodes: ""
- references: ""
- subsystem:
Expand Down Expand Up @@ -212293,7 +212269,7 @@
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- rxnFrom: "HMRdatabase;Recon3D"
- eccodes: ""
- references: ""
- subsystem:
Expand Down Expand Up @@ -219332,7 +219308,6 @@
- MAM00660c: -1
- MAM00660r: -1
- MAM00747r: -1
- MAM00759c: -1
- MAM00828r: -1
- MAM00830c: -1
- MAM00925c: -1
Expand All @@ -219351,6 +219326,7 @@
- MAM01001x: -1
- MAM01011c: -1
- MAM01012c: -1
- MAM01314c: -1
- MAM01792r: -1
- MAM01794r: -1
- MAM02469c: -1
Expand Down Expand Up @@ -251030,25 +251006,6 @@
- subsystem:
- "Fatty acid oxidation"
- confidence_score: 0
- !!omap
- id: "MAR09949"
- name: "Acylcoa Hydrolase, Cytosolic"
- metabolites: !!omap
- MAM01597c: 1
- MAM02039c: 1
- MAM02040c: -1
- MAM02122c: -1
- MAM03684c: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "3.1.2.2"
- references: ""
- subsystem:
- "Fatty acid oxidation"
- confidence_score: 0
- !!omap
- id: "MAR09950"
- name: "Hydrolysis of Tetradecadienoyl Coenzyme A to Cis-5, 8-Tetradecadienoic Acid"
Expand Down Expand Up @@ -256169,8 +256126,8 @@
- MAM01597m: 1
- MAM02039m: 1
- MAM02040m: -1
- MAM02120m: 1
- MAM02122m: -1
- MAM03684m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: ""
Expand Down Expand Up @@ -256220,8 +256177,8 @@
- MAM01597x: 1
- MAM02039x: 1
- MAM02040x: -1
- MAM02120x: 1
- MAM02122x: -1
- MAM03684x: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: ""
Expand Down Expand Up @@ -271773,8 +271730,8 @@
- id: "MAR11290"
- name: "Transport of Hexanoate (N-C6:0), Mitochondrial"
- metabolites: !!omap
- MAM03684c: 1
- MAM03684m: -1
- MAM02120c: 1
- MAM02120m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: ""
Expand All @@ -271789,24 +271746,8 @@
- id: "MAR11291"
- name: "Transport of Hexanoate (N-C6:0), Peroxisome"
- metabolites: !!omap
- MAM03684c: 1
- MAM03684x: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR11292"
- name: "Transport of Hexanoate (N-C6:0), Extracellular"
- metabolites: !!omap
- MAM03684c: -1
- MAM03684e: 1
- MAM02120c: 1
- MAM02120x: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: ""
Expand All @@ -271817,21 +271758,6 @@
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR11293"
- name: "Exchange of Hexanoate (N-C6:0)"
- metabolites: !!omap
- MAM03684e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- subsystem:
- "Exchange/demand reactions"
- confidence_score: 0
- !!omap
- id: "MAR11294"
- name: "Hydrolysis of Fatty Acyl Coenzyme A (14:1)"
Expand Down Expand Up @@ -275993,7 +275919,7 @@
- gene_reaction_rule: ""
- rxnNotes: "https://www.springer.com/gp/book/9789400957800"
- rxnFrom: "Recon3D"
- eccodes: ""
- eccodes: "3.1.2.2"
- references: "PMID:8371066"
- subsystem:
- "Fatty acid oxidation"
Expand Down Expand Up @@ -305941,9 +305867,9 @@
- metabolites: !!omap
- MAM02039c: 2
- MAM02040c: -1
- MAM02120c: 1
- MAM02554c: -1
- MAM02555c: 1
- MAM03684c: 1
- MAM20037c: -1
- lower_bound: 0
- upper_bound: 1000
Expand Down
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